niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3_droimaker.py

@@ -0,0 +1,419 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3_DROIMAKER_METADATA = Metadata(
+    id="52994e672a5f137f27dbb8bbd59f66cee7093ffe.boutiques",
+    name="3DROIMaker",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3DroimakerParameters = typing.TypedDict('V3DroimakerParameters', {
+    "__STYX_TYPE__": typing.Literal["3DROIMaker"],
+    "inset": InputPathType,
+    "thresh": float,
+    "prefix": str,
+    "refset": typing.NotRequired[InputPathType | None],
+    "volthr": typing.NotRequired[float | None],
+    "only_conn_top": typing.NotRequired[float | None],
+    "inflate": typing.NotRequired[float | None],
+    "trim_off_wm": bool,
+    "wm_skel": typing.NotRequired[InputPathType | None],
+    "skel_thr": typing.NotRequired[float | None],
+    "skel_stop": bool,
+    "skel_stop_strict": bool,
+    "csf_skel": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "neigh_upto_vert": bool,
+    "nifti": bool,
+    "preinfl_inset": typing.NotRequired[InputPathType | None],
+    "preinfl_inflate": typing.NotRequired[float | None],
+    "dump_no_labtab": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3DROIMaker": v_3_droimaker_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3DROIMaker": v_3_droimaker_outputs,
+    }.get(t)
+
+
+class V3DroimakerOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3_droimaker(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    gm_map: OutputPathType
+    """GM map of ROIs based on value- and volume-thresholding, corresponding to
+    gray matter regions of activation."""
+    gmi_map: OutputPathType
+    """Map of inflated GM ROIs based on GM map, with ROIs inflated either by
+    user-design or WM skeleton."""
+
+
+def v_3_droimaker_params(
+    inset: InputPathType,
+    thresh: float,
+    prefix: str,
+    refset: InputPathType | None = None,
+    volthr: float | None = None,
+    only_conn_top: float | None = None,
+    inflate: float | None = None,
+    trim_off_wm: bool = False,
+    wm_skel: InputPathType | None = None,
+    skel_thr: float | None = None,
+    skel_stop: bool = False,
+    skel_stop_strict: bool = False,
+    csf_skel: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    neigh_upto_vert: bool = False,
+    nifti: bool = False,
+    preinfl_inset: InputPathType | None = None,
+    preinfl_inflate: float | None = None,
+    dump_no_labtab: bool = False,
+) -> V3DroimakerParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset: 3D volume(s) of values, especially functionally-derived\
+            quantities like correlation values or ICA Z-scores.
+        thresh: Threshold for values in INSET, used to create ROI islands from\
+            the 3D volume's sea of values.
+        prefix: Prefix of output name, with output files being: PREFIX_GM* and\
+            PREFIX_GMI*.
+        refset: 3D (or multi-subbrick) volume containing integer values with\
+            which to label specific GM ROIs after thresholding.
+        volthr: Minimum size a cluster of voxels must have in order to remain a\
+            GM ROI after thresholding. Can reduce 'noisy' clusters.
+        only_conn_top: Select N max contiguous voxels in a region starting from\
+            peak voxel and expanding.
+        inflate: Number of voxels to pad each found ROI in order to turn GM\
+            ROIs into inflated (GMI) ROIs.
+        trim_off_wm: Trim the INSET to exclude voxels in WM by excluding those\
+            which overlap an input WM skeleton.
+        wm_skel: 3D volume containing info of WM, as might be defined from an\
+            FA map or anatomical segmentation.
+        skel_thr: Threshold value for WM skeleton if it is not a mask.
+        skel_stop: Stop inflation at locations which are already on WM\
+            skeleton.
+        skel_stop_strict: Do not allow any inflation into the skel-region.
+        csf_skel: 3D volume containing info of CSF. Info must be a binary mask\
+            already.
+        mask: Mask within which to apply threshold. Useful if the MINTHR is a\
+            negative value.
+        neigh_upto_vert: Define neighbors loosely so that voxels can be grouped\
+            into the same ROI if they share at least one vertex.
+        nifti: Switch to output *.nii.gz GM and GMI files.
+        preinfl_inset: Start with a WM ROI, inflate it to find the nearest GM,\
+            then expand that GM and subtract away the WM+CSF parts.
+        preinfl_inflate: Number of voxels for initial inflation of PSET.
+        dump_no_labtab: Switch for turning off labeltable attachment to the\
+            output GM and GMI files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3DROIMaker",
+        "inset": inset,
+        "thresh": thresh,
+        "prefix": prefix,
+        "trim_off_wm": trim_off_wm,
+        "skel_stop": skel_stop,
+        "skel_stop_strict": skel_stop_strict,
+        "neigh_upto_vert": neigh_upto_vert,
+        "nifti": nifti,
+        "dump_no_labtab": dump_no_labtab,
+    }
+    if refset is not None:
+        params["refset"] = refset
+    if volthr is not None:
+        params["volthr"] = volthr
+    if only_conn_top is not None:
+        params["only_conn_top"] = only_conn_top
+    if inflate is not None:
+        params["inflate"] = inflate
+    if wm_skel is not None:
+        params["wm_skel"] = wm_skel
+    if skel_thr is not None:
+        params["skel_thr"] = skel_thr
+    if csf_skel is not None:
+        params["csf_skel"] = csf_skel
+    if mask is not None:
+        params["mask"] = mask
+    if preinfl_inset is not None:
+        params["preinfl_inset"] = preinfl_inset
+    if preinfl_inflate is not None:
+        params["preinfl_inflate"] = preinfl_inflate
+    return params
+
+
+def v_3_droimaker_cargs(
+    params: V3DroimakerParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dROIMaker")
+    cargs.append(execution.input_file(params.get("inset")))
+    cargs.extend([
+        "-thresh",
+        str(params.get("thresh"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("refset") is not None:
+        cargs.extend([
+            "-refset",
+            execution.input_file(params.get("refset"))
+        ])
+    if params.get("volthr") is not None:
+        cargs.extend([
+            "-volthr",
+            str(params.get("volthr"))
+        ])
+    if params.get("only_conn_top") is not None:
+        cargs.extend([
+            "-only_conn_top",
+            str(params.get("only_conn_top"))
+        ])
+    if params.get("inflate") is not None:
+        cargs.extend([
+            "-inflate",
+            str(params.get("inflate"))
+        ])
+    if params.get("trim_off_wm"):
+        cargs.append("-trim_off_wm")
+    if params.get("wm_skel") is not None:
+        cargs.extend([
+            "-wm_skel",
+            execution.input_file(params.get("wm_skel"))
+        ])
+    if params.get("skel_thr") is not None:
+        cargs.extend([
+            "-skel_thr",
+            str(params.get("skel_thr"))
+        ])
+    if params.get("skel_stop"):
+        cargs.append("-skel_stop")
+    if params.get("skel_stop_strict"):
+        cargs.append("-skel_stop_strict")
+    if params.get("csf_skel") is not None:
+        cargs.extend([
+            "-csf_skel",
+            execution.input_file(params.get("csf_skel"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("neigh_upto_vert"):
+        cargs.append("-neigh_upto_vert")
+    if params.get("nifti"):
+        cargs.append("-nifti")
+    if params.get("preinfl_inset") is not None:
+        cargs.extend([
+            "-preinfl_inset",
+            execution.input_file(params.get("preinfl_inset"))
+        ])
+    if params.get("preinfl_inflate") is not None:
+        cargs.extend([
+            "-preinfl_inflate",
+            str(params.get("preinfl_inflate"))
+        ])
+    if params.get("dump_no_labtab"):
+        cargs.append("-dump_no_labtab")
+    return cargs
+
+
+def v_3_droimaker_outputs(
+    params: V3DroimakerParameters,
+    execution: Execution,
+) -> V3DroimakerOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3DroimakerOutputs(
+        root=execution.output_file("."),
+        gm_map=execution.output_file(params.get("prefix") + "_GM+orig.*.HEAD"),
+        gmi_map=execution.output_file(params.get("prefix") + "_GMI+orig.*.HEAD"),
+    )
+    return ret
+
+
+def v_3_droimaker_execute(
+    params: V3DroimakerParameters,
+    execution: Execution,
+) -> V3DroimakerOutputs:
+    """
+    Create a labelled set of ROIs from input data, useful in combining functional
+    and tractographic/structural data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3DroimakerOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3_droimaker_cargs(params, execution)
+    ret = v_3_droimaker_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3_droimaker(
+    inset: InputPathType,
+    thresh: float,
+    prefix: str,
+    refset: InputPathType | None = None,
+    volthr: float | None = None,
+    only_conn_top: float | None = None,
+    inflate: float | None = None,
+    trim_off_wm: bool = False,
+    wm_skel: InputPathType | None = None,
+    skel_thr: float | None = None,
+    skel_stop: bool = False,
+    skel_stop_strict: bool = False,
+    csf_skel: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    neigh_upto_vert: bool = False,
+    nifti: bool = False,
+    preinfl_inset: InputPathType | None = None,
+    preinfl_inflate: float | None = None,
+    dump_no_labtab: bool = False,
+    runner: Runner | None = None,
+) -> V3DroimakerOutputs:
+    """
+    Create a labelled set of ROIs from input data, useful in combining functional
+    and tractographic/structural data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset: 3D volume(s) of values, especially functionally-derived\
+            quantities like correlation values or ICA Z-scores.
+        thresh: Threshold for values in INSET, used to create ROI islands from\
+            the 3D volume's sea of values.
+        prefix: Prefix of output name, with output files being: PREFIX_GM* and\
+            PREFIX_GMI*.
+        refset: 3D (or multi-subbrick) volume containing integer values with\
+            which to label specific GM ROIs after thresholding.
+        volthr: Minimum size a cluster of voxels must have in order to remain a\
+            GM ROI after thresholding. Can reduce 'noisy' clusters.
+        only_conn_top: Select N max contiguous voxels in a region starting from\
+            peak voxel and expanding.
+        inflate: Number of voxels to pad each found ROI in order to turn GM\
+            ROIs into inflated (GMI) ROIs.
+        trim_off_wm: Trim the INSET to exclude voxels in WM by excluding those\
+            which overlap an input WM skeleton.
+        wm_skel: 3D volume containing info of WM, as might be defined from an\
+            FA map or anatomical segmentation.
+        skel_thr: Threshold value for WM skeleton if it is not a mask.
+        skel_stop: Stop inflation at locations which are already on WM\
+            skeleton.
+        skel_stop_strict: Do not allow any inflation into the skel-region.
+        csf_skel: 3D volume containing info of CSF. Info must be a binary mask\
+            already.
+        mask: Mask within which to apply threshold. Useful if the MINTHR is a\
+            negative value.
+        neigh_upto_vert: Define neighbors loosely so that voxels can be grouped\
+            into the same ROI if they share at least one vertex.
+        nifti: Switch to output *.nii.gz GM and GMI files.
+        preinfl_inset: Start with a WM ROI, inflate it to find the nearest GM,\
+            then expand that GM and subtract away the WM+CSF parts.
+        preinfl_inflate: Number of voxels for initial inflation of PSET.
+        dump_no_labtab: Switch for turning off labeltable attachment to the\
+            output GM and GMI files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3DroimakerOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3_DROIMAKER_METADATA)
+    params = v_3_droimaker_params(
+        inset=inset,
+        thresh=thresh,
+        prefix=prefix,
+        refset=refset,
+        volthr=volthr,
+        only_conn_top=only_conn_top,
+        inflate=inflate,
+        trim_off_wm=trim_off_wm,
+        wm_skel=wm_skel,
+        skel_thr=skel_thr,
+        skel_stop=skel_stop,
+        skel_stop_strict=skel_stop_strict,
+        csf_skel=csf_skel,
+        mask=mask,
+        neigh_upto_vert=neigh_upto_vert,
+        nifti=nifti,
+        preinfl_inset=preinfl_inset,
+        preinfl_inflate=preinfl_inflate,
+        dump_no_labtab=dump_no_labtab,
+    )
+    return v_3_droimaker_execute(params, execution)
+
+
+__all__ = [
+    "V3DroimakerOutputs",
+    "V3DroimakerParameters",
+    "V_3_DROIMAKER_METADATA",
+    "v_3_droimaker",
+    "v_3_droimaker_params",
+]

niwrap_afni/afni/v_3d_aboverlap.py

@@ -0,0 +1,211 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ABOVERLAP_METADATA = Metadata(
+    id="ce33e10c4b1ac12e30e9f2905df1b25512061469.boutiques",
+    name="3dABoverlap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAboverlapParameters = typing.TypedDict('V3dAboverlapParameters', {
+    "__STYX_TYPE__": typing.Literal["3dABoverlap"],
+    "dataset_a": InputPathType,
+    "dataset_b": InputPathType,
+    "no_automask": bool,
+    "quiet": bool,
+    "verbose": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dABoverlap": v_3d_aboverlap_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class V3dAboverlapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_aboverlap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_aboverlap_params(
+    dataset_a: InputPathType,
+    dataset_b: InputPathType,
+    no_automask: bool = False,
+    quiet: bool = False,
+    verbose: bool = False,
+) -> V3dAboverlapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset_a: First input dataset.
+        dataset_b: Second input dataset.
+        no_automask: Consider input datasets as masks (automask does not work\
+            on mask datasets).
+        quiet: Be as quiet as possible (without being entirely mute).
+        verbose: Print out some progress reports (to stderr).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dABoverlap",
+        "dataset_a": dataset_a,
+        "dataset_b": dataset_b,
+        "no_automask": no_automask,
+        "quiet": quiet,
+        "verbose": verbose,
+    }
+    return params
+
+
+def v_3d_aboverlap_cargs(
+    params: V3dAboverlapParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dABoverlap")
+    cargs.append(execution.input_file(params.get("dataset_a")))
+    cargs.append(execution.input_file(params.get("dataset_b")))
+    if params.get("no_automask"):
+        cargs.append("-no_automask")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v_3d_aboverlap_outputs(
+    params: V3dAboverlapParameters,
+    execution: Execution,
+) -> V3dAboverlapOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dAboverlapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_aboverlap_execute(
+    params: V3dAboverlapParameters,
+    execution: Execution,
+) -> V3dAboverlapOutputs:
+    """
+    Counts various metrics about how the automasks of datasets A and B overlap or
+    don't overlap.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAboverlapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_aboverlap_cargs(params, execution)
+    ret = v_3d_aboverlap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_aboverlap(
+    dataset_a: InputPathType,
+    dataset_b: InputPathType,
+    no_automask: bool = False,
+    quiet: bool = False,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> V3dAboverlapOutputs:
+    """
+    Counts various metrics about how the automasks of datasets A and B overlap or
+    don't overlap.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset_a: First input dataset.
+        dataset_b: Second input dataset.
+        no_automask: Consider input datasets as masks (automask does not work\
+            on mask datasets).
+        quiet: Be as quiet as possible (without being entirely mute).
+        verbose: Print out some progress reports (to stderr).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAboverlapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ABOVERLAP_METADATA)
+    params = v_3d_aboverlap_params(
+        dataset_a=dataset_a,
+        dataset_b=dataset_b,
+        no_automask=no_automask,
+        quiet=quiet,
+        verbose=verbose,
+    )
+    return v_3d_aboverlap_execute(params, execution)
+
+
+__all__ = [
+    "V3dAboverlapOutputs",
+    "V3dAboverlapParameters",
+    "V_3D_ABOVERLAP_METADATA",
+    "v_3d_aboverlap",
+    "v_3d_aboverlap_params",
+]